EHV-1 TES dynamics
Balázs Kakuk
## Error in library(future.apply) :
## there is no package called 'future.apply'Project info
Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)
TES dynamics
Those reads were counted only, where the 3-prime adapters were “correct” (according to LoRTIA)
Statistics of counts
Difference from mean
Varcoeff
Clustering of samples
## Bootstrap (r = 0.49)... Done.## Bootstrap (r = 0.6)... Done.## Bootstrap (r = 0.68)... Done.## Bootstrap (r = 0.79)... Done.## Bootstrap (r = 0.89)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.09)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.3)... Done.
## Bootstrap (r = 1.38)... Done.
The sample 48h_3 stands out!
Filtering of samples
Clustering of genes into de-novo clusters using hierarchial clustering
Cluster memberships
## Bootstrap (r = 0.48)... Done.
## Bootstrap (r = 0.59)... Done.
## Bootstrap (r = 0.67)... Done.
## Bootstrap (r = 0.78)... Done.
## Bootstrap (r = 0.89)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.07)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.3)... Done.
## Bootstrap (r = 1.37)... Done.Optimal number of clusters
Find the optimal number of clusters to cut the tree at and calculate
Clustering statistics: Cluster number: 5
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF7, ORF6, ORF5 1.0000000 1.0000000 1.0000000
## 3: 1 ORF10, ORF11 1.0000000 1.0000000 1.0000000
## 4: 1 ORF17 1.0000000 1.0000000 1.0000000
## 5: 1 ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
## 6: 1 ORF30 1.0000000 1.0000000 1.0000000
## 7: 1 ORF31 1.0000000 1.0000000 1.0000000
## 8: 1 ORF32, ORF33, ORF34 1.0000000 1.0000000 1.0000000
## 9: 1 ORF63 1.0000000 1.0000000 1.0000000
## 10: 1 NOIR_1 1.0000000 1.0000000 1.0000000
## 11: 1 ORF65_1 1.0000000 1.0000000 1.0000000
## 12: 1 ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 13: 1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 14: 1 NOIR_2 1.0000000 1.0000000 1.0000000
## 15: 2 ORF2 0.3416432 0.6912340 0.6344858
## 16: 2 ORF3 0.3416432 0.6912340 0.6344858
## 17: 2 ORF8 0.3416432 0.6912340 0.6344858
## 18: 2 ORF9 0.3416432 0.6912340 0.6344858
## 19: 2 ORF12, ORF13, ORF14 0.3416432 0.6912340 0.6344858
## 20: 2 ORF18 0.3416432 0.6912340 0.6344858
## 21: 2 ORF22 0.3416432 0.6912340 0.6344858
## 22: 2 ORF23 0.3416432 0.6912340 0.6344858
## 23: 2 ORF24 0.3416432 0.6912340 0.6344858
## 24: 2 ORF27, ORF26, ORF25 0.3416432 0.6912340 0.6344858
## 25: 2 ORF28, ORF29 0.3416432 0.6912340 0.6344858
## 26: 2 ORF37, ORF36, ORF35, ORF35.5 0.3416432 0.6912340 0.6344858
## 27: 2 ORF36 0.3416432 0.6912340 0.6344858
## 28: 2 ORF37 0.3416432 0.6912340 0.6344858
## 29: 2 ORF38 0.3416432 0.6912340 0.6344858
## 30: 2 ORF39 0.3416432 0.6912340 0.6344858
## 31: 2 CTO 0.3416432 0.6912340 0.6344858
## 32: 2 ORF40 0.3416432 0.6912340 0.6344858
## 33: 2 ORF41, ORF42, OF43 0.3416432 0.6912340 0.6344858
## 34: 2 ORF44 0.3416432 0.6912340 0.6344858
## 35: 2 ORF45, ORF46 0.3416432 0.6912340 0.6344858
## 36: 2 ORF48, ORF49, ORF50, ORF51 0.3416432 0.6912340 0.6344858
## 37: 2 ORF66_1 0.3416432 0.6912340 0.6344858
## 38: 3 ORF4 0.8372572 0.9376206 0.8267637
## 39: 3 ORF69, ORF70 0.8372572 0.9376206 0.8267637
## 40: 4 ORF18, ORF17, ORF16, ORF15 0.9724973 0.9918937 0.9074073
## 41: 4 ORF19 0.9724973 0.9918937 0.9074073
## 42: 4 ORF52 0.9724973 0.9918937 0.9074073
## 43: 4 ORF53, ORF54 0.9724973 0.9918937 0.9074073
## 44: 4 ORF57, ORF58 0.9724973 0.9918937 0.9074073
## 45: 4 ORF62, ORF61, ORF60,ORF59 0.9724973 0.9918937 0.9074073
## 46: 4 ORF71, ORF72, ORF73 0.9724973 0.9918937 0.9074073
## 47: 5 ORF64_1 0.8840047 0.9544882 0.8736200
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 2: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 3: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 4: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 5: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 6: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 7: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 8: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 9: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 10: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 11: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 12: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 13: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 14: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 15: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 16: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 17: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 18: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 19: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 20: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 21: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 22: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 23: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 24: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 25: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 26: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 27: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 28: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 29: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 30: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 31: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 32: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 33: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 34: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 35: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 36: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 37: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 38: 0.021106335 0.010499270 0.004122814 -1.2382778 0.29682443 0.470950264
## 39: 0.021106335 0.010499270 0.004122814 -1.2382778 0.29682443 0.470950264
## 40: 0.005964906 0.002165315 0.003281593 -1.8645245 0.53956761 0.033831486
## 41: 0.005964906 0.002165315 0.003281593 -1.8645245 0.53956761 0.033831486
## 42: 0.005964906 0.002165315 0.003281593 -1.8645245 0.53956761 0.033831486
## 43: 0.005964906 0.002165315 0.003281593 -1.8645245 0.53956761 0.033831486
## 44: 0.005964906 0.002165315 0.003281593 -1.8645245 0.53956761 0.033831486
## 45: 0.005964906 0.002165315 0.003281593 -1.8645245 0.53956761 0.033831486
## 46: 0.005964906 0.002165315 0.003281593 -1.8645245 0.53956761 0.033831486
## 47: 0.017686811 0.008776737 0.003664074 -1.4168469 0.27317558 0.660620818
## se.si se.au se.bp v c pchi
## [1] "ORF44" "ORF48, ORF49, ORF50, ORF51"
## [3] "ORF37, ORF36, ORF35, ORF35.5" "ORF41, ORF42, OF43"## [1] 4## [1] "ORF2" "ORF3"
## [3] "ORF8" "ORF9"
## [5] "ORF12, ORF13, ORF14" "ORF18"
## [7] "ORF22" "ORF23"
## [9] "ORF24" "ORF27, ORF26, ORF25"
## [11] "ORF28, ORF29" "ORF37, ORF36, ORF35, ORF35.5"
## [13] "ORF36" "ORF37"
## [15] "ORF38" "ORF39"
## [17] "CTO" "ORF40"
## [19] "ORF41, ORF42, OF43" "ORF44"
## [21] "ORF45, ORF46" "ORF48, ORF49, ORF50, ORF51"
## [23] "ORF66_1" "ORF4"
## [25] "ORF69, ORF70"## [1] 25Clustering statistics: Cluster number: 6
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF7, ORF6, ORF5 1.0000000 1.0000000 1.0000000
## 3: 1 ORF10, ORF11 1.0000000 1.0000000 1.0000000
## 4: 1 ORF17 1.0000000 1.0000000 1.0000000
## 5: 1 ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
## 6: 1 ORF30 1.0000000 1.0000000 1.0000000
## 7: 1 ORF31 1.0000000 1.0000000 1.0000000
## 8: 1 ORF32, ORF33, ORF34 1.0000000 1.0000000 1.0000000
## 9: 1 ORF63 1.0000000 1.0000000 1.0000000
## 10: 1 NOIR_1 1.0000000 1.0000000 1.0000000
## 11: 1 ORF65_1 1.0000000 1.0000000 1.0000000
## 12: 1 ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 13: 1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 14: 1 NOIR_2 1.0000000 1.0000000 1.0000000
## 15: 2 ORF2 0.3416432 0.6912340 0.6344858
## 16: 2 ORF3 0.3416432 0.6912340 0.6344858
## 17: 2 ORF8 0.3416432 0.6912340 0.6344858
## 18: 2 ORF9 0.3416432 0.6912340 0.6344858
## 19: 2 ORF12, ORF13, ORF14 0.3416432 0.6912340 0.6344858
## 20: 2 ORF18 0.3416432 0.6912340 0.6344858
## 21: 2 ORF22 0.3416432 0.6912340 0.6344858
## 22: 2 ORF23 0.3416432 0.6912340 0.6344858
## 23: 2 ORF24 0.3416432 0.6912340 0.6344858
## 24: 2 ORF27, ORF26, ORF25 0.3416432 0.6912340 0.6344858
## 25: 2 ORF28, ORF29 0.3416432 0.6912340 0.6344858
## 26: 2 ORF37, ORF36, ORF35, ORF35.5 0.3416432 0.6912340 0.6344858
## 27: 2 ORF36 0.3416432 0.6912340 0.6344858
## 28: 2 ORF37 0.3416432 0.6912340 0.6344858
## 29: 2 ORF38 0.3416432 0.6912340 0.6344858
## 30: 2 CTO 0.3416432 0.6912340 0.6344858
## 31: 2 ORF40 0.3416432 0.6912340 0.6344858
## 32: 2 ORF41, ORF42, OF43 0.3416432 0.6912340 0.6344858
## 33: 2 ORF44 0.3416432 0.6912340 0.6344858
## 34: 2 ORF48, ORF49, ORF50, ORF51 0.3416432 0.6912340 0.6344858
## 35: 2 ORF66_1 0.3416432 0.6912340 0.6344858
## 36: 3 ORF4 0.8372572 0.9376206 0.8267637
## 37: 3 ORF69, ORF70 0.8372572 0.9376206 0.8267637
## 38: 4 ORF18, ORF17, ORF16, ORF15 0.9724973 0.9918937 0.9074073
## 39: 4 ORF19 0.9724973 0.9918937 0.9074073
## 40: 4 ORF52 0.9724973 0.9918937 0.9074073
## 41: 4 ORF53, ORF54 0.9724973 0.9918937 0.9074073
## 42: 4 ORF57, ORF58 0.9724973 0.9918937 0.9074073
## 43: 4 ORF62, ORF61, ORF60,ORF59 0.9724973 0.9918937 0.9074073
## 44: 4 ORF71, ORF72, ORF73 0.9724973 0.9918937 0.9074073
## 45: 5 ORF39 0.8840047 0.9544882 0.8736200
## 46: 5 ORF45, ORF46 0.8840047 0.9544882 0.8736200
## 47: 6 ORF64_1 0.2351266 0.6458867 0.5746909
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 2: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 3: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 4: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 5: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 6: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 7: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 8: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 9: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 10: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 11: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 12: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 13: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 14: 0.000000000 0.000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 15: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 16: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 17: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 18: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 19: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 20: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 21: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 22: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 23: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 24: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 25: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 26: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 27: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 28: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 29: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 30: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 31: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 32: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 33: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 34: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 35: 0.037533394 0.026842111 0.005101011 -0.4215546 0.07779672 0.003552515
## 36: 0.021106335 0.010499270 0.004122814 -1.2382778 0.29682443 0.470950264
## 37: 0.021106335 0.010499270 0.004122814 -1.2382778 0.29682443 0.470950264
## 38: 0.005964906 0.002165315 0.003281593 -1.8645245 0.53956761 0.033831486
## 39: 0.005964906 0.002165315 0.003281593 -1.8645245 0.53956761 0.033831486
## 40: 0.005964906 0.002165315 0.003281593 -1.8645245 0.53956761 0.033831486
## 41: 0.005964906 0.002165315 0.003281593 -1.8645245 0.53956761 0.033831486
## 42: 0.005964906 0.002165315 0.003281593 -1.8645245 0.53956761 0.033831486
## 43: 0.005964906 0.002165315 0.003281593 -1.8645245 0.53956761 0.033831486
## 44: 0.005964906 0.002165315 0.003281593 -1.8645245 0.53956761 0.033831486
## 45: 0.017686811 0.008776737 0.003664074 -1.4168469 0.27317558 0.660620818
## 46: 0.017686811 0.008776737 0.003664074 -1.4168469 0.27317558 0.660620818
## 47: 0.037655924 0.028044459 0.005225450 -0.2812843 0.09295466 0.593366429
## se.si se.au se.bp v c pchi
## [1] "ORF27, ORF26, ORF25" "ORF37, ORF36, ORF35, ORF35.5"
## [3] "ORF41, ORF42, OF43"## [1] 3## [1] "ORF2" "ORF3"
## [3] "ORF8" "ORF9"
## [5] "ORF12, ORF13, ORF14" "ORF18"
## [7] "ORF22" "ORF23"
## [9] "ORF24" "ORF27, ORF26, ORF25"
## [11] "ORF28, ORF29" "ORF37, ORF36, ORF35, ORF35.5"
## [13] "ORF36" "ORF37"
## [15] "ORF38" "CTO"
## [17] "ORF40" "ORF41, ORF42, OF43"
## [19] "ORF44" "ORF48, ORF49, ORF50, ORF51"
## [21] "ORF66_1" "ORF4"
## [23] "ORF69, ORF70" "ORF64_1"## [1] 24Clustering statistics: Cluster number: 7
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF7, ORF6, ORF5 1.0000000 1.0000000 1.0000000
## 3: 1 ORF10, ORF11 1.0000000 1.0000000 1.0000000
## 4: 1 ORF17 1.0000000 1.0000000 1.0000000
## 5: 1 ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
## 6: 1 ORF30 1.0000000 1.0000000 1.0000000
## 7: 1 ORF31 1.0000000 1.0000000 1.0000000
## 8: 1 ORF32, ORF33, ORF34 1.0000000 1.0000000 1.0000000
## 9: 1 ORF63 1.0000000 1.0000000 1.0000000
## 10: 1 NOIR_1 1.0000000 1.0000000 1.0000000
## 11: 1 ORF65_1 1.0000000 1.0000000 1.0000000
## 12: 1 ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 13: 1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 14: 1 NOIR_2 1.0000000 1.0000000 1.0000000
## 15: 2 ORF2 0.3416432 0.6912340 0.6344858
## 16: 2 ORF8 0.3416432 0.6912340 0.6344858
## 17: 2 ORF12, ORF13, ORF14 0.3416432 0.6912340 0.6344858
## 18: 2 ORF22 0.3416432 0.6912340 0.6344858
## 19: 2 ORF23 0.3416432 0.6912340 0.6344858
## 20: 2 ORF24 0.3416432 0.6912340 0.6344858
## 21: 2 ORF27, ORF26, ORF25 0.3416432 0.6912340 0.6344858
## 22: 2 ORF37, ORF36, ORF35, ORF35.5 0.3416432 0.6912340 0.6344858
## 23: 2 ORF36 0.3416432 0.6912340 0.6344858
## 24: 2 CTO 0.3416432 0.6912340 0.6344858
## 25: 2 ORF40 0.3416432 0.6912340 0.6344858
## 26: 2 ORF41, ORF42, OF43 0.3416432 0.6912340 0.6344858
## 27: 2 ORF44 0.3416432 0.6912340 0.6344858
## 28: 3 ORF3 0.8372572 0.9376206 0.8267637
## 29: 3 ORF9 0.8372572 0.9376206 0.8267637
## 30: 3 ORF18 0.8372572 0.9376206 0.8267637
## 31: 3 ORF28, ORF29 0.8372572 0.9376206 0.8267637
## 32: 3 ORF37 0.8372572 0.9376206 0.8267637
## 33: 3 ORF38 0.8372572 0.9376206 0.8267637
## 34: 3 ORF48, ORF49, ORF50, ORF51 0.8372572 0.9376206 0.8267637
## 35: 3 ORF66_1 0.8372572 0.9376206 0.8267637
## 36: 4 ORF4 0.9724973 0.9918937 0.9074073
## 37: 4 ORF69, ORF70 0.9724973 0.9918937 0.9074073
## 38: 5 ORF18, ORF17, ORF16, ORF15 0.8840047 0.9544882 0.8736200
## 39: 5 ORF19 0.8840047 0.9544882 0.8736200
## 40: 5 ORF52 0.8840047 0.9544882 0.8736200
## 41: 5 ORF53, ORF54 0.8840047 0.9544882 0.8736200
## 42: 5 ORF57, ORF58 0.8840047 0.9544882 0.8736200
## 43: 5 ORF62, ORF61, ORF60,ORF59 0.8840047 0.9544882 0.8736200
## 44: 5 ORF71, ORF72, ORF73 0.8840047 0.9544882 0.8736200
## 45: 6 ORF39 0.2351266 0.6458867 0.5746909
## 46: 6 ORF45, ORF46 0.2351266 0.6458867 0.5746909
## 47: 7 ORF64_1 0.9954470 0.9985872 0.9770378
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 2: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 3: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 4: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 5: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 6: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 7: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 8: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 9: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 10: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 11: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 12: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 13: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 14: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 15: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 16: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 17: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 18: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 19: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 20: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 21: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 22: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 23: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 24: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 25: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 26: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 27: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 28: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 29: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 30: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 31: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 32: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 33: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 34: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 35: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 36: 0.005964906 0.0021653153 0.003281593 -1.8645245 0.53956761 0.033831486
## 37: 0.005964906 0.0021653153 0.003281593 -1.8645245 0.53956761 0.033831486
## 38: 0.017686811 0.0087767369 0.003664074 -1.4168469 0.27317558 0.660620818
## 39: 0.017686811 0.0087767369 0.003664074 -1.4168469 0.27317558 0.660620818
## 40: 0.017686811 0.0087767369 0.003664074 -1.4168469 0.27317558 0.660620818
## 41: 0.017686811 0.0087767369 0.003664074 -1.4168469 0.27317558 0.660620818
## 42: 0.017686811 0.0087767369 0.003664074 -1.4168469 0.27317558 0.660620818
## 43: 0.017686811 0.0087767369 0.003664074 -1.4168469 0.27317558 0.660620818
## 44: 0.017686811 0.0087767369 0.003664074 -1.4168469 0.27317558 0.660620818
## 45: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 46: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 47: 0.001807476 0.0006553791 0.001781056 -2.4910941 0.49500619 0.107284928
## se.si se.au se.bp v c pchi
## [1] "ORF10, ORF11" "ORF32, ORF33, ORF34" "ORF2"## [1] 3## [1] "ORF2" "ORF8"
## [3] "ORF12, ORF13, ORF14" "ORF22"
## [5] "ORF23" "ORF24"
## [7] "ORF27, ORF26, ORF25" "ORF37, ORF36, ORF35, ORF35.5"
## [9] "ORF36" "CTO"
## [11] "ORF40" "ORF41, ORF42, OF43"
## [13] "ORF44" "ORF3"
## [15] "ORF9" "ORF18"
## [17] "ORF28, ORF29" "ORF37"
## [19] "ORF38" "ORF48, ORF49, ORF50, ORF51"
## [21] "ORF66_1" "ORF39"
## [23] "ORF45, ORF46"## [1] 23Clustering statistics: Cluster number: 10
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF17 1.0000000 1.0000000 1.0000000
## 3: 1 ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
## 4: 1 ORF31 1.0000000 1.0000000 1.0000000
## 5: 1 ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 6: 1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 7: 2 ORF2 0.3416432 0.6912340 0.6344858
## 8: 2 ORF8 0.3416432 0.6912340 0.6344858
## 9: 2 ORF12, ORF13, ORF14 0.3416432 0.6912340 0.6344858
## 10: 2 ORF22 0.3416432 0.6912340 0.6344858
## 11: 2 ORF23 0.3416432 0.6912340 0.6344858
## 12: 2 ORF27, ORF26, ORF25 0.3416432 0.6912340 0.6344858
## 13: 2 ORF37, ORF36, ORF35, ORF35.5 0.3416432 0.6912340 0.6344858
## 14: 2 ORF36 0.3416432 0.6912340 0.6344858
## 15: 2 CTO 0.3416432 0.6912340 0.6344858
## 16: 2 ORF40 0.3416432 0.6912340 0.6344858
## 17: 2 ORF41, ORF42, OF43 0.3416432 0.6912340 0.6344858
## 18: 2 ORF44 0.3416432 0.6912340 0.6344858
## 19: 3 ORF3 0.8372572 0.9376206 0.8267637
## 20: 3 ORF9 0.8372572 0.9376206 0.8267637
## 21: 3 ORF18 0.8372572 0.9376206 0.8267637
## 22: 3 ORF28, ORF29 0.8372572 0.9376206 0.8267637
## 23: 3 ORF37 0.8372572 0.9376206 0.8267637
## 24: 3 ORF38 0.8372572 0.9376206 0.8267637
## 25: 3 ORF48, ORF49, ORF50, ORF51 0.8372572 0.9376206 0.8267637
## 26: 3 ORF66_1 0.8372572 0.9376206 0.8267637
## 27: 4 ORF4 0.9724973 0.9918937 0.9074073
## 28: 4 ORF69, ORF70 0.9724973 0.9918937 0.9074073
## 29: 5 ORF7, ORF6, ORF5 0.8840047 0.9544882 0.8736200
## 30: 5 ORF30 0.8840047 0.9544882 0.8736200
## 31: 5 ORF63 0.8840047 0.9544882 0.8736200
## 32: 5 ORF65_1 0.8840047 0.9544882 0.8736200
## 33: 6 ORF10, ORF11 0.2351266 0.6458867 0.5746909
## 34: 6 ORF32, ORF33, ORF34 0.2351266 0.6458867 0.5746909
## 35: 6 NOIR_1 0.2351266 0.6458867 0.5746909
## 36: 6 NOIR_2 0.2351266 0.6458867 0.5746909
## 37: 7 ORF18, ORF17, ORF16, ORF15 0.9954470 0.9985872 0.9770378
## 38: 7 ORF19 0.9954470 0.9985872 0.9770378
## 39: 7 ORF52 0.9954470 0.9985872 0.9770378
## 40: 7 ORF53, ORF54 0.9954470 0.9985872 0.9770378
## 41: 7 ORF57, ORF58 0.9954470 0.9985872 0.9770378
## 42: 7 ORF62, ORF61, ORF60,ORF59 0.9954470 0.9985872 0.9770378
## 43: 7 ORF71, ORF72, ORF73 0.9954470 0.9985872 0.9770378
## 44: 8 ORF24 0.7336005 0.9384289 0.5284649
## 45: 9 ORF39 0.9967936 0.9992765 0.9533788
## 46: 9 ORF45, ORF46 0.9967936 0.9992765 0.9533788
## 47: 10 ORF64_1 0.2287339 0.6776862 0.5186287
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 2: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 3: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 4: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 5: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 6: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 7: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 8: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 9: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 10: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 11: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 12: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 13: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 14: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 15: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 16: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 17: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 18: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 19: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 20: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 21: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 22: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 23: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 24: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 25: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 26: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 27: 0.005964906 0.0021653153 0.003281593 -1.8645245 0.53956761 0.033831486
## 28: 0.005964906 0.0021653153 0.003281593 -1.8645245 0.53956761 0.033831486
## 29: 0.017686811 0.0087767369 0.003664074 -1.4168469 0.27317558 0.660620818
## 30: 0.017686811 0.0087767369 0.003664074 -1.4168469 0.27317558 0.660620818
## 31: 0.017686811 0.0087767369 0.003664074 -1.4168469 0.27317558 0.660620818
## 32: 0.017686811 0.0087767369 0.003664074 -1.4168469 0.27317558 0.660620818
## 33: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 34: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 35: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 36: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 37: 0.001807476 0.0006553791 0.001781056 -2.4910941 0.49500619 0.107284928
## 38: 0.001807476 0.0006553791 0.001781056 -2.4910941 0.49500619 0.107284928
## 39: 0.001807476 0.0006553791 0.001781056 -2.4910941 0.49500619 0.107284928
## 40: 0.001807476 0.0006553791 0.001781056 -2.4910941 0.49500619 0.107284928
## 41: 0.001807476 0.0006553791 0.001781056 -2.4910941 0.49500619 0.107284928
## 42: 0.001807476 0.0006553791 0.001781056 -2.4910941 0.49500619 0.107284928
## 43: 0.001807476 0.0006553791 0.001781056 -2.4910941 0.49500619 0.107284928
## 44: 0.027805719 0.0093248368 0.005321926 -0.8065648 0.73515322 0.002373838
## 45: 0.001101253 0.0002966973 0.002531325 -2.4318232 0.75328712 0.796418941
## 46: 0.001101253 0.0002966973 0.002531325 -2.4318232 0.75328712 0.796418941
## 47: 0.039354695 0.0269295852 0.005275876 -0.2539753 0.20726302 0.169650471
## se.si se.au se.bp v c pchi
## character(0)## [1] 0## [1] "ORF2" "ORF8"
## [3] "ORF12, ORF13, ORF14" "ORF22"
## [5] "ORF23" "ORF27, ORF26, ORF25"
## [7] "ORF37, ORF36, ORF35, ORF35.5" "ORF36"
## [9] "CTO" "ORF40"
## [11] "ORF41, ORF42, OF43" "ORF44"
## [13] "ORF3" "ORF9"
## [15] "ORF18" "ORF28, ORF29"
## [17] "ORF37" "ORF38"
## [19] "ORF48, ORF49, ORF50, ORF51" "ORF66_1"
## [21] "ORF10, ORF11" "ORF32, ORF33, ORF34"
## [23] "NOIR_1" "NOIR_2"
## [25] "ORF24" "ORF64_1"## [1] 26Clustering statistics: Cluster number: 12
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF17 1.0000000 1.0000000 1.0000000
## 3: 1 ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
## 4: 1 ORF31 1.0000000 1.0000000 1.0000000
## 5: 1 ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 6: 1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 7: 2 ORF2 0.3416432 0.6912340 0.6344858
## 8: 2 ORF40 0.3416432 0.6912340 0.6344858
## 9: 3 ORF3 0.8372572 0.9376206 0.8267637
## 10: 3 ORF9 0.8372572 0.9376206 0.8267637
## 11: 3 ORF18 0.8372572 0.9376206 0.8267637
## 12: 3 ORF28, ORF29 0.8372572 0.9376206 0.8267637
## 13: 3 ORF37 0.8372572 0.9376206 0.8267637
## 14: 3 ORF38 0.8372572 0.9376206 0.8267637
## 15: 3 ORF48, ORF49, ORF50, ORF51 0.8372572 0.9376206 0.8267637
## 16: 3 ORF66_1 0.8372572 0.9376206 0.8267637
## 17: 4 ORF4 0.9724973 0.9918937 0.9074073
## 18: 5 ORF7, ORF6, ORF5 0.8840047 0.9544882 0.8736200
## 19: 5 ORF30 0.8840047 0.9544882 0.8736200
## 20: 5 ORF63 0.8840047 0.9544882 0.8736200
## 21: 5 ORF65_1 0.8840047 0.9544882 0.8736200
## 22: 6 ORF8 0.2351266 0.6458867 0.5746909
## 23: 6 ORF12, ORF13, ORF14 0.2351266 0.6458867 0.5746909
## 24: 6 ORF22 0.2351266 0.6458867 0.5746909
## 25: 6 ORF23 0.2351266 0.6458867 0.5746909
## 26: 6 ORF27, ORF26, ORF25 0.2351266 0.6458867 0.5746909
## 27: 6 ORF37, ORF36, ORF35, ORF35.5 0.2351266 0.6458867 0.5746909
## 28: 6 ORF36 0.2351266 0.6458867 0.5746909
## 29: 6 CTO 0.2351266 0.6458867 0.5746909
## 30: 6 ORF41, ORF42, OF43 0.2351266 0.6458867 0.5746909
## 31: 6 ORF44 0.2351266 0.6458867 0.5746909
## 32: 7 ORF10, ORF11 0.9954470 0.9985872 0.9770378
## 33: 7 ORF32, ORF33, ORF34 0.9954470 0.9985872 0.9770378
## 34: 7 NOIR_1 0.9954470 0.9985872 0.9770378
## 35: 7 NOIR_2 0.9954470 0.9985872 0.9770378
## 36: 8 ORF18, ORF17, ORF16, ORF15 0.7336005 0.9384289 0.5284649
## 37: 8 ORF19 0.7336005 0.9384289 0.5284649
## 38: 8 ORF52 0.7336005 0.9384289 0.5284649
## 39: 8 ORF53, ORF54 0.7336005 0.9384289 0.5284649
## 40: 8 ORF57, ORF58 0.7336005 0.9384289 0.5284649
## 41: 8 ORF62, ORF61, ORF60,ORF59 0.7336005 0.9384289 0.5284649
## 42: 8 ORF71, ORF72, ORF73 0.7336005 0.9384289 0.5284649
## 43: 9 ORF24 0.9967936 0.9992765 0.9533788
## 44: 10 ORF39 0.2287339 0.6776862 0.5186287
## 45: 10 ORF45, ORF46 0.2287339 0.6776862 0.5186287
## 46: 11 ORF64_1 0.2125278 0.7106245 0.4514921
## 47: 12 ORF69, ORF70 0.1340659 0.5964469 0.5293614
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 2: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 3: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 4: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 5: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 6: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 7: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 8: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 9: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 10: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 11: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 12: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 13: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 14: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 15: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 16: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 17: 0.005964906 0.0021653153 0.003281593 -1.8645245 0.53956761 0.033831486
## 18: 0.017686811 0.0087767369 0.003664074 -1.4168469 0.27317558 0.660620818
## 19: 0.017686811 0.0087767369 0.003664074 -1.4168469 0.27317558 0.660620818
## 20: 0.017686811 0.0087767369 0.003664074 -1.4168469 0.27317558 0.660620818
## 21: 0.017686811 0.0087767369 0.003664074 -1.4168469 0.27317558 0.660620818
## 22: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 23: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 24: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 25: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 26: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 27: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 28: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 29: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 30: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 31: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 32: 0.001807476 0.0006553791 0.001781056 -2.4910941 0.49500619 0.107284928
## 33: 0.001807476 0.0006553791 0.001781056 -2.4910941 0.49500619 0.107284928
## 34: 0.001807476 0.0006553791 0.001781056 -2.4910941 0.49500619 0.107284928
## 35: 0.001807476 0.0006553791 0.001781056 -2.4910941 0.49500619 0.107284928
## 36: 0.027805719 0.0093248368 0.005321926 -0.8065648 0.73515322 0.002373838
## 37: 0.027805719 0.0093248368 0.005321926 -0.8065648 0.73515322 0.002373838
## 38: 0.027805719 0.0093248368 0.005321926 -0.8065648 0.73515322 0.002373838
## 39: 0.027805719 0.0093248368 0.005321926 -0.8065648 0.73515322 0.002373838
## 40: 0.027805719 0.0093248368 0.005321926 -0.8065648 0.73515322 0.002373838
## 41: 0.027805719 0.0093248368 0.005321926 -0.8065648 0.73515322 0.002373838
## 42: 0.027805719 0.0093248368 0.005321926 -0.8065648 0.73515322 0.002373838
## 43: 0.001101253 0.0002966973 0.002531325 -2.4318232 0.75328712 0.796418941
## 44: 0.039354695 0.0269295852 0.005275876 -0.2539753 0.20726302 0.169650471
## 45: 0.039354695 0.0269295852 0.005275876 -0.2539753 0.20726302 0.169650471
## 46: 0.042042046 0.0258713272 0.005251072 -0.2166588 0.33855123 0.474259320
## 47: 0.036680782 0.0290517315 0.005268810 -0.1589128 0.08524816 0.261620394
## se.si se.au se.bp v c pchi
## [1] "ORF28, ORF29" "ORF66_1"## [1] 2## [1] "ORF2" "ORF40"
## [3] "ORF3" "ORF9"
## [5] "ORF18" "ORF28, ORF29"
## [7] "ORF37" "ORF38"
## [9] "ORF48, ORF49, ORF50, ORF51" "ORF66_1"
## [11] "ORF8" "ORF12, ORF13, ORF14"
## [13] "ORF22" "ORF23"
## [15] "ORF27, ORF26, ORF25" "ORF37, ORF36, ORF35, ORF35.5"
## [17] "ORF36" "CTO"
## [19] "ORF41, ORF42, OF43" "ORF44"
## [21] "ORF18, ORF17, ORF16, ORF15" "ORF19"
## [23] "ORF52" "ORF53, ORF54"
## [25] "ORF57, ORF58" "ORF62, ORF61, ORF60,ORF59"
## [27] "ORF71, ORF72, ORF73" "ORF39"
## [29] "ORF45, ORF46" "ORF64_1"
## [31] "ORF69, ORF70"## [1] 31Selected number of clusters: 12
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF17 1.0000000 1.0000000 1.0000000
## 3: 1 ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
## 4: 1 ORF31 1.0000000 1.0000000 1.0000000
## 5: 1 ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 6: 1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 7: 2 ORF2 0.3416432 0.6912340 0.6344858
## 8: 2 ORF40 0.3416432 0.6912340 0.6344858
## 9: 3 ORF3 0.8372572 0.9376206 0.8267637
## 10: 3 ORF9 0.8372572 0.9376206 0.8267637
## 11: 3 ORF18 0.8372572 0.9376206 0.8267637
## 12: 3 ORF28, ORF29 0.8372572 0.9376206 0.8267637
## 13: 3 ORF37 0.8372572 0.9376206 0.8267637
## 14: 3 ORF38 0.8372572 0.9376206 0.8267637
## 15: 3 ORF48, ORF49, ORF50, ORF51 0.8372572 0.9376206 0.8267637
## 16: 3 ORF66_1 0.8372572 0.9376206 0.8267637
## 17: 4 ORF4 0.9724973 0.9918937 0.9074073
## 18: 5 ORF7, ORF6, ORF5 0.8840047 0.9544882 0.8736200
## 19: 5 ORF30 0.8840047 0.9544882 0.8736200
## 20: 5 ORF63 0.8840047 0.9544882 0.8736200
## 21: 5 ORF65_1 0.8840047 0.9544882 0.8736200
## 22: 6 ORF8 0.2351266 0.6458867 0.5746909
## 23: 6 ORF12, ORF13, ORF14 0.2351266 0.6458867 0.5746909
## 24: 6 ORF22 0.2351266 0.6458867 0.5746909
## 25: 6 ORF23 0.2351266 0.6458867 0.5746909
## 26: 6 ORF27, ORF26, ORF25 0.2351266 0.6458867 0.5746909
## 27: 6 ORF37, ORF36, ORF35, ORF35.5 0.2351266 0.6458867 0.5746909
## 28: 6 ORF36 0.2351266 0.6458867 0.5746909
## 29: 6 CTO 0.2351266 0.6458867 0.5746909
## 30: 6 ORF41, ORF42, OF43 0.2351266 0.6458867 0.5746909
## 31: 6 ORF44 0.2351266 0.6458867 0.5746909
## 32: 7 ORF10, ORF11 0.9954470 0.9985872 0.9770378
## 33: 7 ORF32, ORF33, ORF34 0.9954470 0.9985872 0.9770378
## 34: 7 NOIR_1 0.9954470 0.9985872 0.9770378
## 35: 7 NOIR_2 0.9954470 0.9985872 0.9770378
## 36: 8 ORF18, ORF17, ORF16, ORF15 0.7336005 0.9384289 0.5284649
## 37: 8 ORF19 0.7336005 0.9384289 0.5284649
## 38: 8 ORF52 0.7336005 0.9384289 0.5284649
## 39: 8 ORF53, ORF54 0.7336005 0.9384289 0.5284649
## 40: 8 ORF57, ORF58 0.7336005 0.9384289 0.5284649
## 41: 8 ORF62, ORF61, ORF60,ORF59 0.7336005 0.9384289 0.5284649
## 42: 8 ORF71, ORF72, ORF73 0.7336005 0.9384289 0.5284649
## 43: 9 ORF24 0.9967936 0.9992765 0.9533788
## 44: 10 ORF39 0.2287339 0.6776862 0.5186287
## 45: 10 ORF45, ORF46 0.2287339 0.6776862 0.5186287
## 46: 11 ORF64_1 0.2125278 0.7106245 0.4514921
## 47: 12 ORF69, ORF70 0.1340659 0.5964469 0.5293614
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 2: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 3: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 4: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 5: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 6: 0.000000000 0.0000000000 0.000000000 0.0000000 0.00000000 0.000000000
## 7: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 8: 0.037533394 0.0268421106 0.005101011 -0.4215546 0.07779672 0.003552515
## 9: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 10: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 11: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 12: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 13: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 14: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 15: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 16: 0.021106335 0.0104992700 0.004122814 -1.2382778 0.29682443 0.470950264
## 17: 0.005964906 0.0021653153 0.003281593 -1.8645245 0.53956761 0.033831486
## 18: 0.017686811 0.0087767369 0.003664074 -1.4168469 0.27317558 0.660620818
## 19: 0.017686811 0.0087767369 0.003664074 -1.4168469 0.27317558 0.660620818
## 20: 0.017686811 0.0087767369 0.003664074 -1.4168469 0.27317558 0.660620818
## 21: 0.017686811 0.0087767369 0.003664074 -1.4168469 0.27317558 0.660620818
## 22: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 23: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 24: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 25: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 26: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 27: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 28: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 29: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 30: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 31: 0.037655924 0.0280444589 0.005225450 -0.2812843 0.09295466 0.593366429
## 32: 0.001807476 0.0006553791 0.001781056 -2.4910941 0.49500619 0.107284928
## 33: 0.001807476 0.0006553791 0.001781056 -2.4910941 0.49500619 0.107284928
## 34: 0.001807476 0.0006553791 0.001781056 -2.4910941 0.49500619 0.107284928
## 35: 0.001807476 0.0006553791 0.001781056 -2.4910941 0.49500619 0.107284928
## 36: 0.027805719 0.0093248368 0.005321926 -0.8065648 0.73515322 0.002373838
## 37: 0.027805719 0.0093248368 0.005321926 -0.8065648 0.73515322 0.002373838
## 38: 0.027805719 0.0093248368 0.005321926 -0.8065648 0.73515322 0.002373838
## 39: 0.027805719 0.0093248368 0.005321926 -0.8065648 0.73515322 0.002373838
## 40: 0.027805719 0.0093248368 0.005321926 -0.8065648 0.73515322 0.002373838
## 41: 0.027805719 0.0093248368 0.005321926 -0.8065648 0.73515322 0.002373838
## 42: 0.027805719 0.0093248368 0.005321926 -0.8065648 0.73515322 0.002373838
## 43: 0.001101253 0.0002966973 0.002531325 -2.4318232 0.75328712 0.796418941
## 44: 0.039354695 0.0269295852 0.005275876 -0.2539753 0.20726302 0.169650471
## 45: 0.039354695 0.0269295852 0.005275876 -0.2539753 0.20726302 0.169650471
## 46: 0.042042046 0.0258713272 0.005251072 -0.2166588 0.33855123 0.474259320
## 47: 0.036680782 0.0290517315 0.005268810 -0.1589128 0.08524816 0.261620394
## se.si se.au se.bp v c pchi
## [1] "ORF28, ORF29" "ORF66_1"## [1] 2## [1] "ORF2" "ORF40"
## [3] "ORF3" "ORF9"
## [5] "ORF18" "ORF28, ORF29"
## [7] "ORF37" "ORF38"
## [9] "ORF48, ORF49, ORF50, ORF51" "ORF66_1"
## [11] "ORF8" "ORF12, ORF13, ORF14"
## [13] "ORF22" "ORF23"
## [15] "ORF27, ORF26, ORF25" "ORF37, ORF36, ORF35, ORF35.5"
## [17] "ORF36" "CTO"
## [19] "ORF41, ORF42, OF43" "ORF44"
## [21] "ORF18, ORF17, ORF16, ORF15" "ORF19"
## [23] "ORF52" "ORF53, ORF54"
## [25] "ORF57, ORF58" "ORF62, ORF61, ORF60,ORF59"
## [27] "ORF71, ORF72, ORF73" "ORF39"
## [29] "ORF45, ORF46" "ORF64_1"
## [31] "ORF69, ORF70"## [1] 31Remove genes from clusters ?
## [1] "ORF2" "ORF40"
## [3] "ORF3" "ORF9"
## [5] "ORF18" "ORF28, ORF29"
## [7] "ORF37" "ORF38"
## [9] "ORF48, ORF49, ORF50, ORF51" "ORF66_1"
## [11] "ORF8" "ORF12, ORF13, ORF14"
## [13] "ORF22" "ORF23"
## [15] "ORF27, ORF26, ORF25" "ORF37, ORF36, ORF35, ORF35.5"
## [17] "ORF36" "CTO"
## [19] "ORF41, ORF42, OF43" "ORF44"
## [21] "ORF18, ORF17, ORF16, ORF15" "ORF19"
## [23] "ORF52" "ORF53, ORF54"
## [25] "ORF57, ORF58" "ORF62, ORF61, ORF60,ORF59"
## [27] "ORF71, ORF72, ORF73" "ORF39"
## [29] "ORF45, ORF46" "ORF64_1"
## [31] "ORF69, ORF70"## [1] 31## No genes were removed from their corresponding clusters.## cluster N
## <int> <int>
## 1: 6 10
## 2: 3 8
## 3: 8 7
## 4: 1 6
## 5: 5 4
## 6: 7 4
## 7: 2 2
## 8: 10 2
## 9: 4 1
## 10: 9 1
## 11: 11 1
## 12: 12 1Merge cluster stats
Assigning genes to clusters
Summarize and melt
Heatmaps
Normalized Expression
Expression delta ~ 6 hpi
Z-score of expression delta ~ 6 hpi
ORF kinetics, according to literature-based kinetic classes
Barplot of mean and SD
Figure 4 REVIEW - Mean and SD with linear connection
Mean and SD with loess function
Mean and SD with linear connection - Figure 4
Each replicate with loess
ORF kinetics, according to de-novo kinetic classes
Mean and SD with linear connection
Figure 5 REVIEW - Mean and SD with linear connection
Compare literature and de novo kinetic classes
NA shows the number of genes where the clustering did not yield an unambiguous result.
Combined Kinetic classes
De Novo Clusters
Literature clusters
